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Search: Single-Cell[Title] AND Transcriptomic[Title] AND Analysis[Title] AND Primary[Title] AND Metastatic[Title] AND Tumor[Title] AND Ecosystems[Title] AND Head[Title] AND Neck[Title] AND Cancer[Title]

Abstract

The diverse malignant, stromal, and immune cells in tumors affect growth, metastasis, and response to therapy. We profiled transcriptomes of ∼6,000 single cells from 18 head and neck squamous cell carcinoma (HNSCC) patients, including five matched pairs of primary tumors and lymph node metastases. Stromal and immune cells had consistent expression programs across patients. Conversely, malignant cells varied within and between tumors in their expression of signatures related to cell cycle, stress, hypoxia, epithelial differentiation, and partial epithelial-to-mesenchymal transition (p-EMT). Cells expressing the p-EMT program spatially localized to the leading edge of primary tumors. By integrating single-cell transcriptomes with bulk expression profiles for hundreds of tumors, we refined HNSCC subtypes by their malignant and stromal composition and established p-EMT as an independent predictor of nodal metastasis, grade, and adverse pathologic features. Our results provide insight into the HNSCC ecosystem and define stromal interactions and a p-EMT program associated with metastasis.

(A) t-SNE plot of malignant cells (as in ) from five primary tumors (black) and their matched LNs (red). Malignant cells cluster by tumor rather than by site.(B) t-SNE plot of non-malignant cells (as in ) from five primary tumors (black) and their matched LNs (red). Non-malignant cells are consistent across tumors but their representation and expression states vary between sites.See .

HNSCC subtypes revised by deconvolution of expression profiles from hundreds of tumors

(A) t-SNE plot of malignant cells from ten tumors (as in ). Each cluster of cells corresponds to a different tumor. Cells are colored according to the TCGA expression subtype that they match. Black indicates no match. Each tumor can be clearly assigned to one of three subtypes: basal, atypical, or classical.(B) t-SNE plot of non-malignant cells (as in ) from ten tumors. Each cluster of cells corresponds to a different cell type. Cells are colored according to the TCGA expression subtype that they match. Black indicates no match. Fibroblasts and myocytes highly express signature genes of the mesenchymal subtype, which likely reflects tumor profiles with high stromal representation.(C) For each TCGA subtype (columns), heatmap shows relative expression of gene signatures for non-malignant cell types (rows), which were used as estimates of cell type abundances. Tumors classified as mesenchymal highly expressed genes specific to CAFs and myocytes, while atypical tumors were enriched for T- and B-cells.(D) Heatmap depicts pairwise correlations between TCGA expression profiles ordered by their subtype annotations. This analysis included all genes and recovered all four subtypes.(E) Schematic of linear regression used to subtract the influence of non-malignant cell frequency from bulk TCGA expression profiles, and thereby infer malignant cell-specific expression profiles.(F) Heatmap depicts pairwise correlations between TCGA expression profiles ordered by their subtype annotations. This analysis was based on the inferred malignant cell-specific expression profiles in (E). Classical and atypical subtypes are maintained. However, basal and mesenchymal subtypes collapse to a single subtype, which we term ‘malignant-basal.’See .